HNRNPA0 RNA-Seq in HepG2

General Information


RBP	HNRNPA0
Cell_Line	HepG2
Method	shRNA
Exp_Name	HNRNPA0-BGHLV22-HepG2
ENCODE_series_ID	ENCSR069UQV
Batch_ID	BGHLV22
Pool ID	Pool-150705
Local_Set_Name	set22
ENCODE_KD_Exp_ID	ENCSR720BPO
ENCODE_CN_Exp_ID	ENCSR279HMU
Rep1	HNRNPA0-BGHLV22-19_17756
Rep2	HNRNPA0-BGHLV22-20_17757
CN1	non-target-BGHLV22-1_17746
CN2	non-target-BGHLV22-2_17747
Rep1_qPCR	59.6
Rep2_qPCR	79.4
Rep1_WB	no clear band
Rep2_WB	no clear band
Antibody Cat#	RN061PW
Antibody Lot#	LOT# 001
Antibody DCC ID	ENCAB119UHC
Status	Released
Project	ENCODE3
ID	536

Experiment Information (Status: Released)

	BGHLV22-19	BGHLV22-20
idx	447	448
TRCN#_or_BGC#	TRCN0000017235	TRCN0000017235
shRNA_or_gRNA_sequence	GCCAAGGTTAAGAAGCTCTTT	GCCAAGGTTAAGAAGCTCTTT
PAM
Name	HNRNPA0	HNRNPA0
Sample_ID	BGHLV22-19	BGHLV22-20
transduction_Date	10/16/2014	10/16/2014
days
RBP_name	HNRNPA0	HNRNPA0
qPCR_result	59.6	79.4
Ave_qPCR	69.5
RT-qPCR_primer-F	ATCGAGCACTTCTCGCAGTT
RT-qPCR_primer-R	ATACACGAAGCCGAATCCAC
protein_conc	6925	6658
WB_result	no clear band	no clear band
Ave_WB
WB_DONE_date	7/21/16	wes
MW	34/36kDa
IP		fu's
antibody_Cat#	RN061PW	RN061PW
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	28.5	0
Rep2_TPM	29.1	0
Action
Library_start_date	6/5/2015	6/5/2015
repeat_library
Note
ID	2516	2517

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHLV22-19	BGHLV22-20
Sample_ID	BGHLV22-19	BGHLV22-20
Sample Name	HNRNPA0-BGHLV22-19_17756	HNRNPA0-BGHLV22-20_17757
Sample Name	HNRNPA0-BGHLV22-19_17756	HNRNPA0-BGHLV22-20_17757
RBP	HNRNPA0	HNRNPA0
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-13	2015-08-13
Project	ENCODE3	ENCODE3
Note
ID	786	787

Library-Prep
Sequencing

Library-Prep Information

	BGHLV22-19	BGHLV22-20
Sample #
Sample Name	HNRNPA0-BGHLV22-19	HNRNPA0-BGHLV22-20
Sample_Name_Alias	HNRNPA0-BGHLV22-19_17756	HNRNPA0-BGHLV22-20_17757
Index Well Position	S11	S12
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-05	2015-06-05
Lib_ID	Lib-150605	Lib-150605
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set1/C7.png	DNA_Library_LV20-22-23/set1/D7.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/C1.png	RNA_Library_LV22-23-25/set1/D1.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV22-19	BGHLV22-20
RBP	HNRNPA0	HNRNPA0
Batch_ID	BGHLV22	BGHLV22
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2472	2473

Sequencing Information

	BGHLV22-19	BGHLV22-20
Sample_ID	BGHLV22-19	BGHLV22-20
Sample Name	HNRNPA0-BGHLV22-19_17756	HNRNPA0-BGHLV22-20_17757
Pool ID	Pool-150705	Pool-150705
LocalServer_folder	set22	set22
total_reads	45,470,000	44,140,000
total_aligned_reads	42,302,230	41,299,894
unique_aligned_reads	39,858,828	38,947,652
percent_uniqueAligned	0.87660	0.88237
correlation_replicates	0.997335	0.997335
spikein_reads	239,986	262,132
percent_spikeins	0.00528	0.00594
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1206	1207

Data Submission Information

	BGHLV22-19	BGHLV22-19
ENCODE_alias	brenton-graveley:HNRNPA0-BGHLV22	brenton-graveley:HNRNPA0-BGHLV22-HepG2
ENCODE_accession	ENCSR720BPO	ENCSR069UQV
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV22-19	BGHLV22-19
Sample Name	HNRNPA0-BGHLV22-19_17756	HNRNPA0-BGHLV22-19_17756
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2925	6746

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	platform	read_length	run_type	paired_end	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
HNRNPA0-BGHLV22-19_17756_GGCTAC_L008_R1_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1206	HiSeq2000	100	paired-ended	1				non-target-BGHLV22-1_17746_ATCACG_L006_R1_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R1_001.fastq.gz	ENCODE3	16282
HNRNPA0-BGHLV22-19_17756_GGCTAC_L008_R2_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1206	HiSeq2000	100	paired-ended	2				non-target-BGHLV22-1_17746_ATCACG_L006_R2_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R2_001.fastq.gz	ENCODE3	16322
HNRNPA0-BGHLV22-19_17756_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1206					GRCh38	V40	HNRNPA0-BGHLV22-19_17756_GGCTAC_L008_R1_001.fastq.gz,HNRNPA0-BGHLV22-19_17756_GGCTAC_L008_R2_001.fastq.gz		ENCORE2	16420
HNRNPA0-BGHLV22-19_17756_Signal.Unique.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1206					GRCh38	V40	HNRNPA0-BGHLV22-19_17756/Aligned.sortedByCoord.out.bam		ENCORE2	16460
HNRNPA0-BGHLV22-19_17756_Signal.Unique.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1206					GRCh38	V40	HNRNPA0-BGHLV22-19_17756/Aligned.sortedByCoord.out.bam		ENCORE2	16500
HNRNPA0-BGHLV22-19_17756_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1206					GRCh38	V40	HNRNPA0-BGHLV22-19_17756/Aligned.sortedByCoord.out.bam		ENCORE2	16540
HNRNPA0-BGHLV22-19_17756_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1206					GRCh38	V40	HNRNPA0-BGHLV22-19_17756/Aligned.sortedByCoord.out.bam		ENCORE2	16580
HNRNPA0-BGHLV22-19_17756_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1206					GRCh38	V40	HNRNPA0-BGHLV22-19_17756_GGCTAC_L008_R1_001.fastq.gz,HNRNPA0-BGHLV22-19_17756_GGCTAC_L008_R2_001.fastq.gz		ENCORE2	16620
HNRNPA0-BGHLV22-20_17757_CTTGTA_L008_R1_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1207	HiSeq2000	100	paired-ended	1				non-target-BGHLV22-1_17746_ATCACG_L006_R1_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R1_001.fastq.gz	ENCODE3	16283
HNRNPA0-BGHLV22-20_17757_CTTGTA_L008_R2_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1207	HiSeq2000	100	paired-ended	2				non-target-BGHLV22-1_17746_ATCACG_L006_R2_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R2_001.fastq.gz	ENCODE3	16323
HNRNPA0-BGHLV22-20_17757_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1207					GRCh38	V40	HNRNPA0-BGHLV22-20_17757_CTTGTA_L008_R1_001.fastq.gz,HNRNPA0-BGHLV22-20_17757_CTTGTA_L008_R2_001.fastq.gz		ENCORE2	16421
HNRNPA0-BGHLV22-20_17757_Signal.Unique.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1207					GRCh38	V40	HNRNPA0-BGHLV22-20_17757/Aligned.sortedByCoord.out.bam		ENCORE2	16461
HNRNPA0-BGHLV22-20_17757_Signal.Unique.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1207					GRCh38	V40	HNRNPA0-BGHLV22-20_17757/Aligned.sortedByCoord.out.bam		ENCORE2	16501
HNRNPA0-BGHLV22-20_17757_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1207					GRCh38	V40	HNRNPA0-BGHLV22-20_17757/Aligned.sortedByCoord.out.bam		ENCORE2	16541
HNRNPA0-BGHLV22-20_17757_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1207					GRCh38	V40	HNRNPA0-BGHLV22-20_17757/Aligned.sortedByCoord.out.bam		ENCORE2	16581
HNRNPA0-BGHLV22-20_17757_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1207					GRCh38	V40	HNRNPA0-BGHLV22-20_17757_CTTGTA_L008_R1_001.fastq.gz,HNRNPA0-BGHLV22-20_17757_CTTGTA_L008_R2_001.fastq.gz		ENCORE2	16621